Small RNAs and their role in biofilm formation

Chambers, Jacob R.; Sauer, Karin

doi:10.1016/j.tim.2012.10.008

Cited by 126 publications

(83 citation statements)

References 101 publications

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“…3E). Similarly, percentage of reads mapping to ncRNAs, which are essential in the modulation of various processes including biofilm formation21, increased ~4-fold in the Ribo-Zero samples relative to the MICROBExpress and RiboMinus samples (Fig. 3E).…”

Section: Resultsmentioning

confidence: 95%

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

Petrova

García-Alcalde

Zampaloni

et al. 2017

Sci Rep

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Global transcriptomic analysis via RNA-seq is often hampered by the high abundance of ribosomal (r)RNA in bacterial cells. To remove rRNA and enrich coding sequences, subtractive hybridization procedures have become the approach of choice prior to RNA-seq, with their efficiency varying in a manner dependent on sample type and composition. Yet, despite an increasing number of RNA-seq studies, comparative evaluation of bacterial rRNA depletion methods has remained limited. Moreover, no such study has utilized RNA derived from bacterial biofilms, which have potentially higher rRNA:mRNA ratios and higher rRNA carryover during RNA-seq analysis. Presently, we evaluated the efficiency of three subtractive hybridization-based kits in depleting rRNA from samples derived from biofilm, as well as planktonic cells of the opportunistic human pathogen Pseudomonas aeruginosa. Our results indicated different rRNA removal efficiency for the three procedures, with the Ribo-Zero kit yielding the highest degree of rRNA depletion, which translated into enhanced enrichment of non-rRNA transcripts and increased depth of RNA-seq coverage. The results indicated that, in addition to improving RNA-seq sensitivity, efficient rRNA removal enhanced detection of low abundance transcripts via qPCR. Finally, we demonstrate that the Ribo-Zero kit also exhibited the highest efficiency when P. aeruginosa/Staphylococcus aureus co-culture RNA samples were tested.

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Section: Resultsmentioning

confidence: 95%

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

Petrova

García-Alcalde

Zampaloni

et al. 2017

Sci Rep

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“…Small RNAs [sRNAs] are known to regulate genes involved in these networks and in the regulation of biofilm formation, with multiple sRNAs regulating expression of FlhDC and CsgD [reviewed in (Chambers and Sauer, ; Mika and Hengge, ; Van Puyvelde et al ., )]. There are at least 90 sRNAs detected in Escherichia coli (Raghavan et al ., ), and a large number of these require the chaperone protein Hfq (De Lay et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Alternative pathways for Escherichia coli biofilm formation revealed by sRNA overproduction

Parker

Cureoglu

Lay

et al. 2017

Molecular Microbiology

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Small regulatory RNAs have major roles in many regulatory circuits in Escherichia coli and other bacteria, including the transition from planktonic to biofilm growth. We tested Hfq-dependent sRNAs in E. coli for their ability, when overproduced, to inhibit or stimulate biofilm formation, in two different growth media. We identify two mutually exclusive pathways for biofilm formation. In LB, PgaA, encoding an adhesion export protein, played a critical role; biofilm was independent of the general stress factor RpoS or CsgD, regulator of curli and other biofilm genes. The PgaA-dependent pathway was stimulated upon overproduction of DsrA, via negative regulation of H-NS, or of GadY, likely by titration of CsrA. In YESCA (Yeast Extract Casamino acids) media, biofilm was dependent upon RpoS and CsgD, but independent of PgaA; RpoS appears to indirectly negatively regulate the PgaA-dependent pathway in YESCA medium. Deletions of most sRNAs had very little effect on biofilm, although deletion of hfq, encoding an RNA chaperone, was defective in both LB and YESCA. Deletion of ArcZ, a small RNA activator of RpoS, decreased biofilm in YESCA; only a portion of this defect could be bypassed by overproduction of RpoS. Overall, sRNAs highlight different pathways to biofilm formation.

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“…Because of their ubiquity and their relevance to medicine and industry, the formation of biofilms has been studied intensively, with an emphasis on the genes, regulatory mechanisms, and transport properties that underlie transitions from planktonic growth to surface attachment (15)(16)(17), to proliferation and matrix secretion (2,18), and finally to dispersal (19,20). A basic understanding of several regulatory circuits and secreted matrix components governing biofilm formation has been developed (21)(22)(23)(24)(25). Nonetheless, the physical, biological, and chemical factors that interact to determine the biofilm architecture remain largely unknown.…”

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Architectural transitions in Vibrio cholerae biofilms at single-cell resolution

Drescher

Dunkel

Nadell

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Many bacterial species colonize surfaces and form dense 3D structures, known as biofilms, which are highly tolerant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. Here, we use high-resolution optical microscopy to image all individual cells in Vibrio cholerae biofilms at different stages of development, including colonies that range in size from 2 to 4,500 cells. From these data, we extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. We discovered several critical transitions of the internal and external biofilm architectures that separate the major phases of V. cholerae biofilm growth. Optical imaging of biofilms with single-cell resolution provides a new window into biofilm formation that will prove invaluable to understanding the mechanics underlying biofilm development.biofilm | community | self-organization | emergent order | nematic order

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Small RNAs and their role in biofilm formation

Cited by 126 publications

References 101 publications

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

Alternative pathways for Escherichia coli biofilm formation revealed by sRNA overproduction

Architectural transitions in Vibrio cholerae biofilms at single-cell resolution

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